Skip to main content

Table 2 Decreases in the numbers of near native structures for all types of protein complexes

From: IFACEwat: the interfacial water-implemented re-ranking algorithm to improve the discrimination of near native structures for protein rigid docking

#

Wi = 0

Number of hits found (in %)a and level of hit decrease

  

A

AB

E

O

0

(W 1 ,W 2 ,W 3 ,W 4 )

100

100

100

100

1

(0,W2,W3,W4)

↓↓↓↓ (41.5)

↓↓ (87.5)

↓↓ (73.8)

↓↓ (74.4)

2

(W1,0,W3,W4)

-

↓↓ (75.0)

↓ (97.1)

↓ (98.2)

3

(W1,W2,0,W4)

-

-

↓ (97.0)

↓ (98.0)

4

(W1,W2,W3,0)

↓↓↓↓ (17.1)

↓↓↓ (37.5)

↓↓ (78.0)

↓↓ (90.0)

5

(W1,0,0,W4)b

-

↓↓ (87.5)

↓ (97.0)

↓ (97.7)

6

(0,W2,W3,0)

↓↓↓↓↓ (4.87)

↓↓↓ (50.0)

↓↓↓↓ (30.0)

↓↓↓↓ (18.7)

7

(0,0,0,W4)

↓↓↓↓ (43.9)

↓↓ (75.0)

↓↓ (71.9)

↓↓ (75.8)

8

(W1,0,0,0)

↓↓↓↓ (17.0)

↓↓↓↓↓ (0.0)

↓↓ (74.2)

↓↓ (89.0)

  1. Antigen/unbound-Antibody (A), Antigen/bound-Antibody (AB), Enzyme/Inhibitor (E) and others (O): ↓ (less than 5% hits drop), ↓↓ (less than 30% hits drop), ↓↓↓ (noticeably drop less than 50% hits), ↓↓↓↓ (significantly drop less than 70% hits), ↓↓↓↓↓ (dramatically drop more than 95% hits), - (unchanged). Experiment #0 shows the results of number of hits obtained from the full set of weights (w 1 , w 2 , w 3 , w 4 ) for each complex type and is used as the reference (in bold). a% of hits as compared to the reference (i.e. results of the experiment #0) bOnly 4 combinations (#5 to #8) of weights are presented to highlight the significant contributions of w1 and w4